Frequently Asked Questions

1. What is the main difference between IsoBase and other ortholog databases?

IsoBase has been developed by global network alignment on multiple PPI networks. We demonstrate that incorporating PPI network data in ortholog prediction results in improvements over existing sequence-only approaches and over predictions from local alignments. In addition, our network alignment tools outperform existing algorithms for global network alignment in coverage and consistency on multiple alignments of the five available eukaryotic PPI networks.

2. How does IsoBase generate functional orthologs across multiple species?

We used the global PPI network alignment tools, IsoRank & IsoRankN,  based on the idea similar to PageRank and graph spectral clustering to detect and generate functional orthologs for IsoBase. We also evaluated the biological relevance of our prediction against two gene ontology databases: GO and KEGG.

3. What ortholog information is provided?

For each ortholog across multiple species, the brief information such as constituent protein names and their respective synonyms, is provided. Moreover, we give the entropy of every ortholog/cluster to represent the consistency. That is, a cluster has lower entropy if its GO and KEGG annotations are more within-cluster consistent. The GO and KEGG categories the constituent proteins belong to are also shown.

4. Why does IsoBase collect orthologs from only five Eukaryotic species?

IsoBase is a collection of functional orthologs predicted by our network alignment tools. Hence we only provide the orthologs from five available eukaryotic PPI networks so far. The functional orthologs across prokaryotic species (PPI networks) will be presented in the near future. With the increasing availability of large PPI networks, IsoBase would collect orthologs from more species.

5. How can I cite IsoBase?

If you would like to cite IsoBase, the references are given as follows.
1. Rohit Singh, Jinbo Xu, and Bonnie Berger. (2008) Global alignment of multiple protein interaction networks with application to functional orthology detection, Proc. Natl. Acad. Sci. USA 105:12763-12768.
2. Chung-Shou Liao, Kanghao Lu, Michael Baym, Rohit Singh, and Bonnie Berger. (2009) IsoRankN: Spectral methods for global alignment of multiple protein networks, in Proc. of the 17th International Conference on Intelligent Systems for Molecular Biology (ISMB). Invited to Bioinformatics 2009 25(12):i253-i258.